Evidence of Australian wild deer exposure to N. caninum infection and potential implications for the maintenance of N. caninum sylvatic cycle.

Infections with the coccidian parasite Neospora caninum affect domestic and wild animals worldwide. In Australia, N. caninum infections cause considerable losses to the cattle industry with seroprevalence of 8.7% in beef and 10.9% in dairy cattle. Conversely, the role of wild animals, in maintaining the parasite cycle is also unclear. It is possible that native or introduced herbivorous species could be reservoir hosts of N. caninum in Australia, but to date, this has not been investigated. We report here the first large-scale screening of N. caninum antibodies in Australian wild deer, spanning three species (fallow, red and sambar deer). Consequently, we also assessed two commercial cELISA tests validated for detecting N. caninum in cattle for their ability to detect N. caninum antibodies in serum samples of wild deer. N. caninum antibodies were detected in 3.7% (7/189, 95% CI 1.8 - 7.45) of the wild deer serum samples collected in south-eastern Australia (n = 189), including 97 fallow deer (Dama dama), 14 red deer (Cervus elaphus), and 78 sambar deer (Rusa unicolor). Overall, our study provides the first detection of N. caninum antibodies in wild deer and quantifies deer's potential role in the sylvatic cycle of N. caninum.

Post-weaning survival in kangaroos is high and constant until senescence: Implications for population dynamics.

Large herbivores typically have consistently high prime-aged adult survival and lower, more variable, juvenile, and senescent survival. Many kangaroo populations undergo greater fluctuations in density compared with other large herbivores, but age- and sex-specific survival of kangaroos and their response to environmental variation remain poorly estimated. We used long-term capture-mark-recapture data on 920 individuals to investigate the survival component of eastern grey kangaroo (Macropus giganteus) population dynamics. Forage availability and population density were monitored quarterly and included as predictors of survival in Bayesian Cormack-Jolly-Seber models. Annual survival probabilities were estimated for five age classes: 0 years (juveniles), 1-2 years (subadults), 3-6 years (prime-aged adults), 7-9 years (presenescent adults), and ≥10 years (senescent adults). Survival of juveniles varied widely during our 12-year study, ranging from 0.07 to 0.90 for females and 0.05-0.92 for males. Subadult survival was 0.80-0.93 for females and 0.75-0.85 for males, while that of prime-aged adults was ≥0.94 for females and ≥0.83 for males, despite large fluctuations in forage and density. The survival of presenescent adults spanned 0.86-0.93 for females and 0.60-0.86 for males. Senescent survival was variable, at 0.49-0.90 for females and 0.49-0.80 for males. Male survival was significantly lower than female survival in prime-aged and presenescent adults, but not in other age classes. Although most of the models supported by Watanabe-Akaike Information Criterion selection included at least one environmental covariate, none of these covariates individually had a discernible effect on survival. Temporal variability in overall survival appeared mostly due to changes in the survival of juvenile and senescent kangaroos. Kangaroo survival patterns are similar to those of ungulates, suggesting a strong role of sex-age structure on population dynamics.

Estimating deer density and abundance using spatial mark-resight models with camera trap data.

Globally, many wild deer populations are actively studied or managed for conservation, hunting, or damage mitigation purposes. These studies require reliable estimates of population state parameters, such as density or abundance, with a level of precision that is fit for purpose. Such estimates can be difficult to attain for many populations that occur in situations that are poorly suited to common survey methods. We evaluated the utility of combining camera trap survey data, in which a small proportion of the sample is individually recognizable using natural markings, with spatial mark-resight (SMR) models to estimate deer density in a variety of situations. We surveyed 13 deer populations comprising four deer species (Cervus unicolor, C. timorensis, C. elaphus, Dama dama) at nine widely separated sites, and used Bayesian SMR models to estimate population densities and abundances. Twelve surveys provided sufficient data for analysis and seven produced density estimates with coefficients of variation (CVs) ≤ 0.25. Estimated densities ranged from 0.3 to 24.6 deer km-2. Camera trap surveys and SMR models provided a powerful and flexible approach for estimating deer densities in populations in which many detections were not individually identifiable, and they should provide useful density estimates under a wide range of conditions that are not amenable to more widely used methods. In the absence of specific local information on deer detectability and movement patterns, we recommend that at least 30 cameras be spaced at 500-1,000 m and set for 90 days. This approach could also be applied to large mammals other than deer.

Detection and Characterisation of an Endogenous Betaretrovirus in Australian Wild Deer.

Endogenous retroviruses (ERVs) are the remnants of past retroviral infections that once invaded the host's germline and were vertically transmitted. ERV sequences have been reported in mammals, but their distribution and diversity in cervids are unclear. Using next-generation sequencing, we identified a nearly complete genome of an endogenous betaretrovirus in fallow deer (Dama dama). Further genomic analysis showed that this provirus, tentatively named cervid endogenous betaretrovirus 1 (CERV ß1), has typical betaretroviral genome features (gag-pro-pol-env) and the betaretrovirus-specific dUTPase domain. In addition, CERV ß1 pol sequences were detected by PCR in the six non-native deer species with wild populations in Australia. Phylogenetic analyses demonstrated that CERV ß1 sequences from subfamily Cervinae clustered as sister taxa to ERV-like sequences in species of subfamily Muntiacinae. These findings, therefore, suggest that CERV ß1 endogenisation occurred after the split of these two subfamilies (between 3.3 and 5 million years ago). Our results provide important insights into the evolution of betaretroviruses in cervids.

Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia.

The use of high-throughput sequencing has facilitated virus discovery in wild animals and helped determine their potential threat to humans and other animals. We report the complete genome sequence of a novel picornavirus identified by next-generation sequencing in faeces from Australian fallow deer. Genomic analysis revealed that this virus possesses a typical picornavirus-like genomic organisation of 7554 nt with a single open reading frame (ORF) encoding a polyprotein of 2225 amino acids. Based on the amino acid identity comparison and phylogenetic analysis of the P1, 2C, 3CD, and VP1 regions, this novel picornavirus was closely related to but distinct from known bopiviruses detected to date. This finding suggests that deer/bopivirus could belong to a novel species within the genus Bopivirus, tentatively designated as "Bopivirus C". Epidemiological investigation of 91 deer (71 fallow, 14 sambar and 6 red deer) and 23 cattle faecal samples showed that six fallow deer and one red deer (overall prevalence 7.7%, 95% confidence interval [CI] 3.8-15.0%) tested positive, but deer/bopivirus was undetectable in sambar deer and cattle. In addition, phylogenetic and sequence analyses indicate that the same genotype is circulating in south-eastern Australia. To our knowledge, this study reports for the first time a deer-origin bopivirus and the presence of a member of genus Bopivirus in Australia. Further epidemiological and molecular studies are needed to investigate the geographic distribution and pathogenic potential of this novel Bopivirus species in other domestic and wild animal species.

Molecular Epidemiology and Characterization of Picobirnavirus in Wild Deer and Cattle from Australia: Evidence of Genogroup I and II in the Upper Respiratory Tract.

Picobirnaviruses (PBVs) have been detected in several species of animals worldwide; however, data pertaining to their presence in Australian wild and domestic animals are limited. Although PBVs are mostly found in faecal samples, their detection in blood and respiratory tract samples raises questions concerning their tropism and pathogenicity. We report here PBV detection in wild deer and cattle from southeastern Australia. Through metagenomics, the presence of PBV genogroups I (GI) and II (GII) were detected in deer serum and plasma. Molecular epidemiology studies targeting the partial RNA-dependent RNA polymerase gene were performed in a wide range of specimens (serum, faeces, spleen, lung, nasal swabs, and trachea) collected from wild deer and cattle, with PCR amplification obtained in all specimen types except lung and spleen. Our results reveal the predominance of GI and concomitant detection of both genogroups in wild deer and cattle. In concordance with other studies, the detected GI sequences displayed high genetic diversity, however in contrast, GII sequences clustered into three distinct clades. Detection of both genogroups in the upper respiratory tract (trachea and nasal swab) of deer in the present study gives more evidence about the respiratory tract tropism of PBV. Although much remains unknown about the epidemiology and tropism of PBVs, our study suggests a wide distribution of these viruses in southeastern Australia.

Evaluation of haemoparasite and Sarcocystis infections in Australian wild deer.

Wild animals are natural reservoir hosts for a variety of pathogens that can be transmitted to other wildlife, livestock, other domestic animals, and humans. Wild deer (family Cervidae) in Europe, Asia, and North and South America have been reported to be infected with gastrointestinal and vector-borne parasites. In Australia, wild deer populations have expanded considerably in recent years, yet there is little information regarding which pathogens are present and whether these pathogens pose biosecurity threats to humans, wildlife, livestock, or other domestic animals. To address this knowledge gap, PCR-based screening for five parasitic genera was conducted in blood samples (n = 243) sourced from chital deer (Axis axis), fallow deer (Dama dama), rusa deer (Rusa timorensis) and sambar deer (Rusa unicolor) sampled in eastern Australia. These blood samples were tested for the presence of DNA from Plasmodium spp., Trypanosoma spp., Babesia spp., Theileria spp. and Sarcocystis spp. Further, the presence of antibodies against Babesia bovis was investigated in serum samples (n = 105) by immunofluorescence. In this study, neither parasite DNA nor antibodies were detected for any of the five genera investigated. These results indicate that wild deer are not currently host reservoirs for Plasmodium, Trypanosoma, Babesia, Theileria or Sarcocystis parasites in eastern Australia. We conclude that in eastern Australia, wild deer do not currently play a significant role in the transmission of these parasites. This survey represents the first large-scale molecular study of its type in Australian wild deer and provides important baseline information about the parasitic infection status of these animals. The expanding populations of wild deer throughout Australia warrant similar surveys in other parts of the country and surveillance efforts to continually assess the level of threat wild deer could pose to humans, wildlife, livestock and other domestic animals.

Serosurveillance and Molecular Investigation of Wild Deer in Australia Reveals Seroprevalence of Pestivirus Infection.

Since deer were introduced into Australia in the mid-1800s, their wild populations have increased in size and distribution, posing a potential risk to the livestock industry, through their role in pathogen transmission cycles. In comparison to livestock, there are limited data on viral infections in all wildlife, including deer. The aim of this study was to assess blood samples from wild Australian deer for serological evidence of exposure to relevant viral livestock diseases. Blood samples collected across eastern Australia were tested by ELISA to detect antigens and antibodies against Pestivirus and antibodies against bovine herpesvirus 1. A subset of samples was also assessed by RT-PCR for Pestivirus, Simbu serogroup, epizootic hemorrhagic disease virus and bovine ephemeral fever virus. Our findings demonstrated a very low seroprevalence (3%) for ruminant Pestivirus, and none of the other viruses tested were detected. These results suggest that wild deer may currently be an incidental spill-over host (rather than a reservoir host) for Pestivirus. However, deer could be a future source of viral infections for domestic animals in Australia. Further investigations are needed to monitor pathogen activity and quantify possible future infectious disease impacts of wild deer on the Australian livestock industry.

Correction to: Forage availability and maternal characteristics affect costs of reproduction in a large marsupial.

Unfortunately, the online publication contained an error in the "Data availability statement" and it is corrected by this erratum.

Forage availability and maternal characteristics affect costs of reproduction in a large marsupial.

Life history theory predicts trade-offs in allocation between survival, maintenance, growth, and reproduction, especially when resources are scarce. Individual variation in resource acquisition can affect trade-offs, but is often unaccounted for. We quantified the fitness costs of reproduction, accounting for environmental conditions, maternal characteristics and individual variation. We analyzed 10 years of data from marked kangaroos to evaluate how reproductive allocation affected annual mass change and skeletal growth, subsequent fecundity and weaning success, and survival, accounting for maternal mass or size and forage availability. Through repeated measurements of 76-91 females, we investigated how trade-offs varied within and between individuals, assessing whether individual variation could mask population-level trade-offs. In poor environments, females that weaned an offspring lost mass. Females that nursed an offspring for > 7 months had reduced skeletal growth. Females that did not gain mass over the previous 12 months rarely reproduced, especially if they had nursed an offspring for > 7 months the previous year. Reproductive allocation had no effect on weaning success, which was very low, and did not affect maternal survival, suggesting a conservative strategy. Disentangling within- and between-individual responses revealed trade-offs within individuals, but because individuals did not vary in their responses to earlier effort, these trade-offs did not drive population trends. The interacting effects of environmental conditions, maternal characteristics and individual variation on allocation trade-offs demonstrate the importance of long-term monitoring for understanding life history variations in changing environments.

Komodo dragons are not ecological analogs of apex mammalian predators.

Apex predators can have substantial and complex ecological roles in ecosystems. However, differences in species-specific traits, population densities, and interspecific interactions are likely to determine the strength of apex predators' roles. Here we report complementary studies examining how interactions between predator per capita metabolic rate and population density influenced the biomass, population energy use, and ecological effects of apex predators on their large mammalian prey. We first investigated how large mammal prey resources and field metabolic rates of terrestrial apex predators, comprising large mammals and the Komodo dragon (Varanus komodoensis), influenced their biomass densities and population energy use requirements. We next evaluated whether Komodo dragons, like apex mammalian predators, exerted top-down regulation of their large mammal prey. Comparison of results from field studies demonstrates that Komodo dragons attain mean population biomass densities that are 5.75-231.82 times higher than that of apex mammalian predator species and their guilds in Africa, Asia, and North America. The high biomass of Komodo dragons resulted in 1.96-108.12 times greater population energy use than that of apex mammalian predators. Nevertheless, substantial temporal and spatial variation in Komodo dragon population energy use did not regulate the population growth rates of either of two large mammal prey species, rusa deer (Rusa timorensis) and wild pig (Sus scrofa). We suggest that multiple processes weaken the capacity of Komodo dragons to regulate large mammal prey populations. For example, a low per capita metabolic rate requiring an infrequent and inactive hunting strategy (including scavenging), would minimize lethal and nonlethal impacts on prey populations. We conclude that Komodo dragons differ in their predatory role from, including not being the ecological analogs of, apex mammalian predators.

The Australian National Rabbit Database: 50 yr of population monitoring of an invasive species.

With ongoing introductions into Australia since the 1700s, the European rabbit (Oryctolagus cuniculus) has become one of the most widely distributed and abundant vertebrate pests, adversely impacting Australia's biodiversity and agroeconomy. To understand the population and range dynamics of the species and its impacts better, occurrence and abundance data have been collected by researchers and citizens from sites covering a broad spectrum of climatic and environmental conditions in Australia. The lack of a common and accessible repository for these data has, however, limited their use in determining important spatiotemporal drivers of the structure and dynamics of the geographical range of rabbits in Australia. To meet this need, we created the Australian National Rabbit Database, which combines more than 50 yr of historical and contemporary survey data collected from throughout the range of the species in Australia. The survey data, obtained from a suite of complementary monitoring methods, were combined with high-resolution weather, climate, and environmental information, and an assessment of data quality. The database provides records of rabbit occurrence (689,265 records) and abundance (51,241 records, >120 distinct sites) suitable for identifying the spatiotemporal drivers of the rabbit's distribution and for determining spatial patterns of variation in its key life-history traits, including maximum rates of population growth. Because all data are georeferenced and date stamped, they can be coupled with information from other databases and spatial layers to explore the potential effects of rabbit occurrence and abundance on Australia's native wildlife and agricultural production. The Australian National Rabbit Database is an important tool for understanding and managing the European rabbit in its invasive range and its effects on native biodiversity and agricultural production. It also provides a valuable resource for addressing questions related to the biology, success, and impacts of invasive species more generally. No copyright or proprietary restrictions are associated with the use of this data set other than citation of this Data Paper.

How many to sample? Statistical guidelines for monitoring animal welfare outcomes.

There is increasing scrutiny of the animal welfare impacts of all animal use activities, including agriculture, the keeping of companion animals, racing and entertainment, research and laboratory use, and wildlife management programs. A common objective of animal welfare monitoring is to quantify the frequency of adverse animal events (e.g., injuries or mortalities). The frequency of such events can be used to provide pass/fail grades for animal use activities relative to a defined threshold and to identify areas for improvement through research. A critical question in these situations is how many animals should be sampled? There are, however, few guidelines available for data collection or analysis, and consequently sample sizes can be highly variable. To address this question, we first evaluated the effect of sample size on precision and statistical power in reporting the frequency of adverse animal welfare outcomes. We next used these findings to assess the precision of published animal welfare investigations for a range of contentious animal use activities, including livestock transport, horse racing, and wildlife harvesting and capture. Finally, we evaluated the sample sizes required for comparing observed outcomes with specified standards through hypothesis testing. Our simulations revealed that the sample sizes required for reasonable levels of precision (i.e., proportional distance to the upper confidence interval limit (δ) of ≤ 0.50) are greater than those that have been commonly used for animal welfare assessments (i.e., >300). Larger sample sizes are required for adverse events with low frequency (i.e., <5%). For comparison with a required threshold standard, even larger samples sizes are required. We present guidelines, and an online calculator, for minimum sample sizes for use in future animal welfare assessments of animal management and research programs.

Exploring mechanisms and origins of reduced dispersal in island Komodo dragons.

Loss of dispersal typifies island biotas, but the selective processes driving this phenomenon remain contentious. This is because selection via, both indirect (e.g. relaxed selection or island syndromes) and direct (e.g. natural selection or spatial sorting) processes may be involved, and no study has yet convincingly distinguished between these alternatives. Here, we combined observational and experimental analyses of an island lizard, the Komodo dragon (Varanus komodoensis, the world's largest lizard), to provide evidence for the actions of multiple processes that could contribute to island dispersal loss. In the Komodo dragon, concordant results from telemetry, simulations, experimental translocations, mark-recapture, and gene flow studies indicated that despite impressive physical and sensory capabilities for long-distance movement, Komodo dragons exhibited near complete dispersal restriction: individuals rarely moved beyond the valleys they were born/captured in. Importantly, lizard site-fidelity was insensitive to common agents of dispersal evolution (i.e. indices of risk for inbreeding, kin and intraspecific competition, and low habitat quality) that consequently reduced survival of resident individuals. We suggest that direct selection restricts movement capacity (e.g. via benefits of spatial philopatry and increased costs of dispersal) alongside use of dispersal-compensating traits (e.g. intraspecific niche partitioning) to constrain dispersal in island species.

Cost-Effective Large-Scale Occupancy-Abundance Monitoring of Invasive Brushtail Possums (Trichosurus Vulpecula) on New Zealand's Public Conservation Land.

There is interest in large-scale and unbiased monitoring of biodiversity status and trend, but there are few published examples of such monitoring being implemented. The New Zealand Department of Conservation is implementing a monitoring program that involves sampling selected biota at the vertices of an 8-km grid superimposed over the 8.6 million hectares of public conservation land that it manages. The introduced brushtail possum (Trichosurus Vulpecula) is a major threat to some biota and is one taxon that they wish to monitor and report on. A pilot study revealed that the traditional method of monitoring possums using leg-hold traps set for two nights, termed the Trap Catch Index, was a constraint on the cost and logistical feasibility of the monitoring program. A phased implementation of the monitoring program was therefore conducted to collect data for evaluating the trade-off between possum occupancy-abundance estimates and the costs of sampling for one night rather than two nights. Reducing trapping effort from two nights to one night along four trap-lines reduced the estimated costs of monitoring by 5.8% due to savings in labour, food and allowances; it had a negligible effect on estimated national possum occupancy but resulted in slightly higher and less precise estimates of relative possum abundance. Monitoring possums for one night rather than two nights would provide an annual saving of NZ$72,400, with 271 fewer field days required for sampling. Possums occupied 60% (95% credible interval; 53-68) of sampling locations on New Zealand's public conservation land, with a mean relative abundance (Trap Catch Index) of 2.7% (2.0-3.5). Possum occupancy and abundance were higher in forest than in non-forest habitats. Our case study illustrates the need to evaluate relationships between sampling design, cost, and occupancy-abundance estimates when designing and implementing large-scale occupancy-abundance monitoring programs.

Solar Radiation Determines Site Occupancy of Coexisting Tropical and Temperate Deer Species Introduced to New Zealand Forests.

Assemblages of introduced taxa provide an opportunity to understand how abiotic and biotic factors shape habitat use by coexisting species. We tested hypotheses about habitat selection by two deer species recently introduced to New Zealand's temperate rainforests. We hypothesised that, due to different thermoregulatory abilities, rusa deer (Cervus timorensis; a tropical species) would prefer warmer locations in winter than red deer (Cervus elaphus scoticus; a temperate species). Since adult male rusa deer are aggressive in winter (the rut), we also hypothesised that rusa deer and red deer would not use the same winter locations. Finally, we hypothesised that in summer both species would prefer locations with fertile soils that supported more plant species preferred as food. We used a 250 × 250 m grid of 25 remote cameras to collect images in a 100-ha montane study area over two winters and summers. Plant composition, solar radiation, and soil fertility were also determined for each camera location. Multiseason occupancy models revealed that direct solar radiation was the best predictor of occupancy and detection probabilities for rusa deer in winter. Multistate, multiseason occupancy models provided strong evidence that the detection probability of adult male rusa deer was greater in winter and when other rusa deer were present at a location. Red deer mostly vacated the study area in winter. For the one season that had sufficient camera images of both species (summer 2011) to allow two-species occupancy models to be fitted, the detection probability of rusa deer also increased with solar radiation. Detection probability also varied with plant composition for both deer species. We conclude that habitat use by coexisting tropical and temperate deer species in New Zealand likely depends on the interplay between the thermoregulatory and behavioural traits of the deer and the abiotic and biotic features of the habitat.

Adoption in eastern grey kangaroos: a consequence of misdirected care?

Adoption is rare in animals and is usually attributed to kin selection. In a 6-year study of eastern grey kangaroos (Macropus giganteus), 11 of 326 juveniles were adopted. We detected eight adoptions by observing behavioural associations and nursing between marked mothers and young and three more by analysing the relatedness of mothers and young using microsatellite DNA. Four adoptions involved reciprocal switches and three were by mothers whose own pouch young were known to subsequently disappear. Adoptive mothers were not closely related to each other or to adoptees but adoptive mothers and young associated as closely as did biological pairs, as measured by half-weight indices. Switch mothers did not associate closely. Maternal age and body condition did not influence the likelihood of adoption but females were more likely to adopt in years with high densities of females with large pouch young. Adoption did not improve juvenile survival. We conclude that adoptions in this wild population were potentially costly and likely caused by misdirected care, suggesting that eastern grey kangaroos may have poorly developed mother-offspring recognition mechanisms.

Interspecific and geographic variation in the diets of sympatric carnivores: dingoes/wild dogs and red foxes in south-eastern Australia.

Dingoes/wild dogs (Canis dingo/familiaris) and red foxes (Vulpes vulpes) are widespread carnivores in southern Australia and are controlled to reduce predation on domestic livestock and native fauna. We used the occurrence of food items in 5875 dingo/wild dog scats and 11,569 fox scats to evaluate interspecific and geographic differences in the diets of these species within nine regions of Victoria, south-eastern Australia. The nine regions encompass a wide variety of ecosystems. Diet overlap between dingoes/wild dogs and foxes varied among regions, from low to near complete overlap. The diet of foxes was broader than dingoes/wild dogs in all but three regions, with the former usually containing more insects, reptiles and plant material. By contrast, dingoes/wild dogs more regularly consumed larger mammals, supporting the hypothesis that niche partitioning occurs on the basis of mammalian prey size. The key mammalian food items for dingoes/wild dogs across all regions were black wallaby (Wallabia bicolor), brushtail possum species (Trichosurus spp.), common wombat (Vombatus ursinus), sambar deer (Rusa unicolor), cattle (Bos taurus) and European rabbit (Oryctolagus cuniculus). The key mammalian food items for foxes across all regions were European rabbit, sheep (Ovis aries) and house mouse (Mus musculus). Foxes consumed 6.1 times the number of individuals of threatened Critical Weight Range native mammal species than did dingoes/wild dogs. The occurrence of intraguild predation was asymmetrical; dingoes/wild dogs consumed greater biomass of the smaller fox. The substantial geographic variation in diet indicates that dingoes/wild dogs and foxes alter their diet in accordance with changing food availability. We provide checklists of taxa recorded in the diets of dingoes/wild dogs and foxes as a resource for managers and researchers wishing to understand the potential impacts of policy and management decisions on dingoes/wild dogs, foxes and the food resources they interact with.